The Legend of Zelda: Trials with Time
by emzzz101
Summary: 7 years after the defeat of Ganondorf, Link returns to Hyrule to settle down and live a peaceful life.  But, he soon finds that there is new evil afoot, and he must help protect the land and the Goddesses. Looks like Link is going to need a partner!
1. Chapter 1

**Hi! I'm Emily, and I just wanted to share with everyone a story that has been going on in my head for about 2 years now. I have always loved Zelda, and I would always imagine what would happen after everything in my two favourite N64 games (I haven't tried the new game…as I don't have a Wii ******

**But anyways, I know this will seem like a slow start, but please give me some feedback on this story, and what you think of it so far! This will take place after MM and will not incorporate anything from any of the games after that, sorry! Thank you very much! OH, and of course…**

**Disclaimer: I don't own anything about Zelda, I just like imagining stories about it in my head :D**

Heavy boots fell upon the damp earth with deep thuds, disturbing the birds that flew into the air at the sound. Out of the mist that engulfed the Lost Woods emerged a young man, with blonde hair and blue eyes, wearing Kokiri clothing of dark green. The Hero, Link, walked out of the woods, and set his eyes on the village that he had not seen for seven years, the village of the Kokiri children. It seemed to him that nothing had changed, the same children from seven years before remained as children, and still did the same things that they had done when Link was a child with them.

Except Link had changed. He had grown up; he was not a Kokiri like he believed himself to be long ago. He remembered to when the New Deku Tree had told him that he was a Hyrulian, after he had defeated the Forest Temple, how impossible the quest he had to complete seemed, and how much he had learned about himself. He laughed to himself taking in the sight before him. He had no need to worry about temples anymore. After his adventures in Clock Town, and after travelling around the vast world around him, he had decided that he had had enough. It was time to settle down, maybe run a farm, or gain a real job. He was a hero that was not needed anymore. There was no Ganondorf, or Majora.

He sighed and walked through the village; the children all stopped their jobs and took in the sight of seeing an actual adult in their lands. None of them recognised him, and Link did not want to try to explain who he really was, so he ducked his head and swiftly moved through the village to the passage that took him to the only person that he could go to for advice, for help.

The sun blinded him as he walked into the bright Hyrule field. His eyes stung after the sun being so dim underneath the foliage of the trees. But as Link's eyes adjusted and he looked around, he saw that it seemed that also here nothing had changed. He could not believe how similar everything was even after so much time had passed. The giant farm, owned by Malon's family, stood in the centre of Hyrule field. To the North lay the mountains and Death Mountain with its ring of smoke. The Zora River still floated lazily past, leading from the East where the Zoras resided. And to the West, though not in sight, he knew lay the desert in which the Gerudo, the all-women tribe, resided. He spotted what he needed first though: a sparkling white castle in the distance, and he headed towards it.

As he entered the market, the bustling of the townspeople reminded him of Clock Town, which was so full of life. Like there, nobody recognised that this was the hero who saved them all from the Dark King, for they had gone back in time so none of the travesties that occurred were known to anyone but him. So he walked through the town, like any other person, and made his way to the castle.

'No matter how much dung you tell me about how you know the Queen, I am not going to let you in!' The guard stood his ground at the iron gates that stood between Link and his one friend for any distance.

'But you don't understand…I know the Princess, I mean, Queen…And she knows me, just go tell her that Link needs to talk to her-'

'Ha! You think I'm going to get in trouble for disturbing the Queen over a commoner like you? Get lost!' Link, stood there, fuming. But finally, he remembered about something he had kept from long ago, something that was somewhat sacred to him. He remembered back to so long ago, when Zelda had handed him a letter to get him into the top of Death Mountain…Link pulled the letter out of his shirt, and handed it to the guard, reminding himself of so long ago…The guard stared at the letter then relented, 'Fine, you may go through, but I'm watching you,' he turned to his other guard, 'take this man to the castle.' Link reluctantly thanked the man, and the other, younger, guard took Link through the gate,

'Don't listen to that other guard, his head just grew three times bigger when he gained a higher position as a guard, we're not all like that.' Link smiled at the man. The guard looked at his clothing, 'So where exactly are you from, that's not the normal fashion I see in the market, though I must even question what some people there wear.' Link looked at his trusty fighting gear, did he really look that odd?

'I was originally from here, but I have been travelling for many years around the world, so I guess I got accustomed to other clothing.' The guard acknowledged his statement, and they arrived at the heavy drawbridge that was (supposedly) the only way into the castle.

'Sorry about the high security here,' the guard said, 'but you can't beat this security, this is the only way someone can get in or out of this castle.'

'Ah, I see, very nice,' said Link as he tried to keep the humour out of his voice. Link sure did know another way to get into this castle…

After the guard talked to another guard, the drawbridge lowered, and for the first time he began to feel a bit nervous about what was about to happen. He hadn't seen Zelda for seven years, and now she was Queen of Hyrule. A lot had changed. Thinking of royalty, he looked at his quite grubby clothes, and tried to tidy his hair up under his cap. He hoped he didn't look unacceptable for a Queen. But it didn't seem to be as a servant led Link, once he was in the castle, to a seating area. Link had never been in the castle, and he could not believe the richness of it, the gold, the ancient artefacts, it was an amazing castle. Once he was seated in a chair that seemed to be painted in gold, yet the cushions were made of burgundy velvet, the servant bowed to him,

'The Queen will be with you soon, she is in a meeting at the moment. May I get you anything to drink?' Link declined and he was left alone in the giant room.

Just as he was about to get sick of waiting around, the door opened, and in walked the woman Link had not seen for so long. Her long, blonde hair fell to her mid-back, and her beautiful pale skin shone in the light as if she was heavenly. She wore a beautiful dark blue dress, with the Triforce designed around the edges and on her chest. She was just as beautiful as he always remembered. She looked taken aback at the sight of Link.

'When my servant told me a boy named Link had come, I did not dare believe for a moment that it was you…but it is!' She came up to Link, and Link jumped from his chair and bowed. 'Oh please do not insult me with bowing to me, you are my friend!' She hugged Link, and the smell of lavender ran into Link's nostrils. Once they had both sat down, she turned to him, 'Where have you been? I have not heard anything from you for seven long years. I thought for a while that you would never be coming back…'

'I have been travelling the world, I have defeated other enemies in other lands, and I've just been searching the world; trying to find my place…' Link sighed, 'But now it is time that I came back to where I belong, to my home. I just wanted to hear from someone I trusted about what has changed. Since the timeline has of course changed since when Ganondorf existed, I guessed that things are different from the present we saw when Ganondorf ruled.'

'You are quite right to think so,' Zelda said, 'Hyrule has prospered since you have left, until a bit ago we were becoming stronger, and more united, than we had ever been before. We have new lands that were brought together to be called a part of the land of Hyrule. New species! We have fairies, but not like Navi, they are almost human-like, with the feathers of birds, and creatures that are more humanlike than the Zora's but also similar to fish, far past the realm of the Zora's. A lot has changed.

'I have also learned more about this land being Queen. I have seen that there are more than just Sages and the three goddesses, Nayru, Din, and Farore, protecting our land. I have found out from ancient passages that there are also Demi-Gods, in a way, that the Sages are actually supposed to serve. They also protect this world, but are more powerful than Sages, and deep within our land, hidden, are the castles and temples in which they reside, giving their power to keep Hyrule in balance. I have seen one of them once…Since I am a sage, as you know, I saw a beautiful woman, a Demi-Goddess, that resided in the land near the fairies, in the Sacred Realm. She called herself the Goddess of the Wind, and that was all she said to me. I guess they only appear when they are absolutely needed. They do not even present themselves to their own Sage servants.' She sighed and smiled at Link, 'Sorry, this must be quite a lot to take in.'

'No I'm fine. Well, it seems we won't need these Goddesses anytime in the future...' Link saw Zelda's expression, full of anxiety, and worry, '…will we?'

Zelda stood up and walked to the window overlooking Hyrule, 'Something dark is appearing upon these lands. I fear that it might still be Ganondorf.' Link started to speak but Zelda interrupted him, 'You forget that he still has the Triforce of Power, even in the realm that we have trapped him in. With that sort of power he could be manipulating the world outside from his prison. This discovery of more Goddesses has frightened me. What happens if he knows more than us about them? We do not know what he could be capable of. And we cannot take anything for granted. We must be weary of anything that changes, even in this land, or within the realm in which Ganondor is captured.' She smiled at link, 'I am glad that you have returned, it's nice to have someone to talk to who realises the true power of Ganondorf.'

'So where are the sages? If you are afraid of Ganondorf somehow getting to the Goddesses then why not have the sages do their job and protect the Goddesses?'

Zelda sighed, 'I cannot do that to them. The sages also have duties outside of this one; Ruto is Queen of the Zoras. Darunia is King of the Gorons…We cannot just keep to this single job. I could only ask them for their help if I was certain of something going on. But all I have now is a hunch. I would not worry about it for now Link…So what are you going to do now that you are back here? I could get you a job here in the castle, or like we joked seven years ago, you could be the Royal Messenger.'

'I think I want to start up a farm, somewhere near the forest, which was my home for so long. After so long I am ready to settle down,' Link stood up as did Zelda, 'Thank you for explaining this all to me, and expressing your concerns. If you do figure out anything else about Ganondorf, and if he is up to anything, you'll know where to find me, and I will put it as my first duty to help you,' The servant entered the room and stood waiting to lead Link out of the castle, 'Goodbye your Majesty, until we meet again.'

'Thank you Link, I hope our next meeting is not as long as a gap as this last one has been. I will contact you if I learn of anything. Goodbye.'

Link stood on the hill leading up to Hyrule castle, and he watched the sun, oozing what almost seemed like blood from its pores, set along the horizon. Link started walking away from the castle, and was ready to start a very different life from the one that he had been living for so long…

_**Next Chapter: Six months has passed in Hyrule since the day the Hero of Time had once again met the Queen of Hyrule. What has happened to Link and his dreams of a quiet life? Was the threat of Ganondorf real, is he really up to anything?? Find out in the next chapter of **__**The Legend of Zelda: Trials with Time,**__** 'The Messenger'**_


	2. The Messenger

**Hello everyone! Sorry it took me a bit longer than I thought to post a new chapter but here it is! Thank you for my reviews, they made me want to write more. Disclaimer: I do not own Zelda. So here it is, **_**Chapter Two: the Messenger**_

'Here's your money for your crops sir, and I hope that we can do business in the future,' said the salesman in the Market, smiling at Link. Link smiled back, and left the shop, walking out into the busy market. He sighed, and looked around him at everyone else, and thought to himself how he was now like any other person in Hyrule. He was no hero anymore.

Link watched the sun sitting on the horizon as he sat on Epona, riding to his home.

'Not far now Epona, almost home,' he patted her neck, and looked at the house appearing in the distance. Link was happy with the house he had made, a quaint, white, straw-thatched house, which was cosy on cold, dark nights. The house was located near the entrance to Lake Hylia, yet hidden somewhat in the woods surrounding the lake, giving Link some of the privacy that he had always liked. Plus Link had plenty of land, which he used to grow all the crops that he needed for money, and for his own stomach.

Link put Epona in her stable, gave her some hay, and stumbled into his house. It had been a long day; he was glad that he only needed to go a few times a year to the Market. Link sipped on a bottle of milk from Malon's farm, enjoying this time to relax, and he thought about the last few months. Everything that he had wanted for some time he now had, he was able to live peacefully, and not have to worry about any dark encounters, or quests that were on the brink of suicide for him. He had a peaceful life now; nobody can do the job of hero forever. Link, lost in his thoughts, jumped when he saw that it was now midnight, and he needed to be up early for some more harvesting tomorrow. Link walked to the little bedroom that was adjacent to the sitting room and kitchen, and after changing, lay down in his bed, and looked at the ceiling through the darkness of night. He was happy, of course he was, and he would be even more when he got more used to this sort of life. It was a big change for him. Link was worried for a couple months that he would have Sages coming to his house, telling him of how Ganondorf has returned, and that he would have to set off again. But luckily, he guessed that what Zelda had felt before was just a false alarm. Closing his eyes, Link felt more at ease, and let sleep take over him…

_Darkness. That was all that Link saw around him. Dark brooding storms brawled above him, lightning striking at the ground. This world seemed to personify evil. He looked around what seemed like a completely different Hyrule to the one that he knew; everything was dead, the grass, the trees. It seemed that all life had been taken from this beautiful land. What had happened for this to occur?_

_Suddenly Link got a feeling in his gut that always meant that there was more to this than he had previously thought. It seemed that his thoughts, and body, without his control, were urging him on to Hyrule castle in the distance, to the Market. Link ran as fast as he could in the direction, but as he levelled up to the bridge, he saw that something else lay before them, and it was not until he was closer to them, that his blood ran cold at what he saw._

_Bodies. Bodies of Hyrulians, Zora, Kokiri, Goron…They were all piled among each other, all with looks of pain and fear etched upon their cold, dead faces. The smell that wafted through Link's nose made him gag. Friend's faces stood out like a sore thumb among the bodies; Darunia, Ruto, and (making him nearly cry out) Saria. Link fell to his knees in front of the pile of dead bodies, and he looked up at the top of the hundreds of bodies. On the top of the pile stood someone Link never thought he would see again. Ganondofr, in full fighting armour, stood on the bodies, looking at Link with a look of pure joy at what he had done. He chuckled darkly, and kicked a head of a Kokiri child that lay dead near his feet._

_'Do you like what I've done with the place, Hero of Time?' Ganondorf asked, smiling his most wicked smile, 'This is all because you tried to foil my plans; you tried to stop the inevitable. But you were too late, Hero, you were too late for your friends. I now have all the pieces of the Triforce, and now no one can ever stop me.' Showing his hand to Link, the three pieces of the Triforce gleamed, but were also somewhat dimmed. 'You've stopped me countless times before this one, and you have destroyed my plans so many times. It was time I partially returned the favour to you.' _

_From behind him, Ganondorf, pulled out a girl that Link had never met before, in fact, he had never met anyone like her. She had feathered wings growing out of her back as if she was partially mixed with a bird. She had brown flowing hair, which was tied back, and bright blue eyes, that at this moment, were full of defeat. She had seemed to have donned the clothing of the Gerudos, yet she was not one herself. She was beautiful. And yet, though Link had never met this woman, his heart felt like it was being squeezed by Ganondorf himself when he saw Ganondorf holding her. Ganondorf, pulled out a black sword from a sheath at his side, and put it to the girl's neck, who showed no feelings of fear on her face; she just stared at Link. Ganondorf looked up at Link and smiled, 'You have taken many precious things from me in the past, and now, I will take something precious from you,' while smiling at Link, he brought the sword deeply across the girl's neck. As blood gushed from her neck, Ganondorf let go of her, and she seemed to be still watching Link as she fell forward, dead._

'NOOOOOOOOOOOOOOOO!' Link screamed and shot up in bed. It took Link a minute to realise where he was. He was taking quick, short breaths, and he tried to calm himself down. It was just a dream, nothing more. Drenched in sweat, he thought back to the dream he just had. It couldn't mean anything, he was just overreacting. He had had dreams like this before, dreams that seemed so real to him. Before they had just been dreams too. Link laughed to himself at this point, he was lying to himself. He thought back to his dreams about seeing Ganondorf before, and nearly that exact event he had dreamt had occurred. This was different, he told himself, Ganondorf was safely locked into the Sacred Realm, so there was no need to worry. Yet as he lied back down, feeling much calmer now, he could not get the blue eyes of that girl out of his head.

Link wiped the sweat off his brow, and looked proudly at his fine creation. That was the fifth batch of hay that he had rolled together today. If he kept up at this rate, he would be going to market again much quicker than he thought. Link rolled the hay into the stables where he stored it, and thought about what his next job was. He had not fed his chickens today. Link questioned whether he should just let the damn things starve; he fed them, spent his money on them, yet they never seemed to produce any eggs for him. He collected the chicken feed and walked to the pen, and started scattering the seeds on the floor, to the chicken's delight. While throwing the seed, he looked up at the sky. The dark clouds he saw reminded him so much of the dream last night. He wondered why he was still thinking about that silly dream, and laughed. A minute or too later though, he felt the hairs on the back of his neck stand on end, as if someone was watching him. Turning around, he spotted, on the hill near his house, a figure, shrouded in a dark cloak that even covered their face. The ominous feeling from the figure put link on edge, and felt on his side for his trusty blade. It was nothing compared to the Master Sword, but it was good for any normal tasks.

'Can I help you?' Asked Link, as the figure moved down the hill towards him at a frighteningly quick pace. The figure did not answer, and Link assumed the worst. This person was going to attack him. Link jumped over the chicken fence and faced his enemy, holding the blade for battle, but just as he was about to lunge at the enemy, the figure stopped, and pulled down its hood. Link stopped in mid-motion, nearly falling over, as he saw the face of Zelda emerge from the hood. Her face was gaunt with worry, she had dark circles under her eyes, and this did nothing to calm Link's nerves. 'What's wrong?' He asked, putting his blade away.

'Keep that blade out, you do not know when you might be using it,' said Zelda, looking over her shoulder, 'I came to you as soon as I could. I thought I had more time, but I was so wrong. We have been deceived this whole time, it was right under our noses, yet me, and the other Sages; we did not see or sense a thing! We were so foolish…'

'Wait, wait wait. Start from the beginning, I am confused, what has happened?' asked Link. Zelda paused and looked at his face,

'Do you not feel it? The presence in the air? Evil is upon us, much sooner than all of us thought possible. It's Ganondorf, Link, he has fooled us all. All this time we thought he could do nothing where he was trapped, but it seems the Triforce of Power is even more powerful than we previously thought. It seems like he can send out his spirit, even though he is in the dark realm, to come to our world, to do the deeds that he needs doing. He has been using his spirit to gain power over this world, and none of us noticed it. I have been talking to all the Sages, and none of them noticed a thing.

'With his spirit, and some dark magic, that I know nothing about, he has gained even more power than before, and with what seems like no tools, he has created himself a sword, a sword of pure malice, the blade is black like his soul-'Link's stomach lurched at this description, and in his mind flashed the sword that Ganondorf bore in his dream, matching the exact description of the one mentioned now. '-Link, he's escaped from his prison with this sword, he has slashed his way through the way guarding him. I just managed to escape from the castle, before…before he got there. It is just like last time, he walks a free man, but I know that he has more ambition than ever before.

'I told you about the Demi-Goddesses, and how I thought that Ganondorf somehow also knew about their power. This sword that he bears now, with it, he will be able to do anything, he will take over this land! Link you must help us, don again your battle gear, and work with the Goddesses that are in this world, and destroy Ganondorf for good. He deserves no prison this time, just full out-right execution. The Goddesses have heard my pleas, and will lend you their power, so that you can go defeat the dark King.'

From within her cloak, Zelda pulled out the sword that Link had missed so much. The gleaming Master Sword, sat with all its glory in Zelda's hands, and she put her hands out to Link, waiting for him to take the sword. 'Go to him now Link, and finish the job that was started so long ago. I will come with you and help as much as I can. We do not have a minute to lose. You must put on your gear, and we must go.'

Link looked at the sword that Zelda was holding out towards him, waiting for him to accept. He could not go back to his days of a hero; he had told himself that he would put them behind him. But as he thought back to his dream last night, he knew that even if he was unwilling to do the task, he must do it to save the people of Hyrule. He regretfully picked up the sword, and ran inside, and put on the gear he had not worn for quite a while, yet it still fit perfectly. Running back outside to Zelda, he noticed that she had once again, pulled up the hood of her clock to hide her face. 'Good, let's go.'

Together they ran to the direction of the castle. And what he saw nearly made Link stop in his tracks. In the distance he could see the once pearl-white castle up in flames, and a dark miasma had seemed to surround the entire area. They were getting closer now, closer to finally being able to live a normal life, without this bastard disrupting him anymore.

Yet just as he had said this, Zelda stopped abruptly, and clutched her head, in agony.

'What's wrong!?' Asked Link, going over to her. Her eyes were squeezed shut, and suddenly her sage mark was glowing pink on forehead.

'Ganondorf…it…cannot be…' Suddenly to their left, from an area deep within the woods, a yellow beam seemingly shot out from nowhere in the ground, and as though this had a chain reaction, beams of different colours shot out from different areas of Hyrule. Green from the Kokiri forest, red from the mountains, purple from the East, blue from near the Zoras, black from Kakariko village, and orange from the West. 'Ganondorf, he has captured the Goddesses,' said Zelda, looking up in anguish, 'he has taken their powers, and sealed them so that they cannot help you. We cannot fight now, it is fight or flight, and he is too powerful for even you now. We must hide. Quick, before he finds you! We must not be seen! Look, there's a grotto hole over there, jump in.

The two ran over to the hole, and shot down, falling onto a bed of flowers. Sitting down in the dark dungeon, Zelda sat on a log and put her face in her hands. 'We were too late,' she said, 'he beat us to the Goddesses, and now we cannot gain their help. Even time is against us now, as he captured the Goddess of Time too.' Zelda's symbol on her head continued to gleam brightly. 'I cannot stay here, it is too dangerous, and being a sage, I must help try to fix this world in ways that you cannot. I must go to the sacred realms, with Rauru, and help in spiritual ways.'

'Well, what am I supposed to do?' Link asked, staring at her, 'I can defeat Ganondorf, but I cannot defeat him with the power of Goddesses on his side…'

'You already know what I am going to ask of you Hero of Time,' said Zelda, 'you must do what you have to. You must go to the temples of the Goddesses, not the Sage's temples, and you must free the Goddesses from the prison that Ganondorf has put them in. With that freedom, Ganondorf will lose their power, and once they are all free, they will put their power in you to defeat him. I am sorry but it is the only way.' Link looked down, feeling once again the dread of the impossible sounding quest that stood in his future. 'Link…' said Zelda hesitating, 'you will do this, won't you? For the good of Hyrule?' Link looked at her, and saw the anticipation on her face.

'…Of course I will,' said Link, regretfully, 'where should I start?' Zelda gained a look of relief on her face, and said,

'Start with the Goddess of the Wind, who resides with the winged fairies I told you about, past the Kokiri woods, in the great, ancient depths of the forest. There you will find the fairies, and the temple. You will know from there what to do next. But now Link, I must leave you, and deal with the problems I bear with being a sage. I am sorry I cannot travel with you, I'm sure you understand. Make sure you stay hidden as you travel in the open Hyrule field, you do not want to be seen by spies. Goodbye Link, and good luck. May the Goddesses still be on your side.' And with that she walked up to Link and placed a kiss on his cheek, and Link felt like his face was on fire. Zelda smiled, and faded away right in front of him. Then she was gone.

Link climbed out of the grotto hole, and looked at Hyrule, which seemed to him, was starting to look more like it did in his dream. Link stood straight, and faced the direction of the Kokiri Forest, and started walking. Walking to a new challenge, and a new Quest, which seemed more impossible than any other challenge he had faced.

_**Coming in the next chapter… Link Travels to the land of the feathered beings new to the land of Hyrule, and finds that it's not only the missing Goddess that the fairies have to deal with…They have problems of their own! It seems like they will not lead Link to the temple unless they get his help first! See all this and more in Chapter 3 of **__**Legend of Zelda: Trials with Time**__**: War.**_

_**Please Review!**_


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